Health experts say the three-dose vaccine is most effective when given to girls as young as 9.

“We are already providing HPV vaccine in school-based clinics,” city Deputy Health Commissioner Isaac Weisfuse said at a City Council Health Committee hearing.

Dr. Weisfuse did not specify how much of the vaccine was distributed to school clinics but said it was important to provide the vaccine in schools because teens normally don’t see doctors frequently.

“Because adolescents do not utilize the primary-care system as regularly as younger children, we are identifying alternative sites to maximize access to vaccine . . . School-based clinics and after-school programs will be recruited for the VFC [Vaccines for Children] program,” he said.

The city’s public hospital system also said it would also help administer the vaccine in schools.

“That’s something we are exploring,” said Dr. Ramanathan Raju, vice president and chief medical officer of the Health and Hospitals Corp.

“We should probably look at middle schools and high schools.”

The federal Vaccines for Children program provides free vaccines to girls age 9 through 18 who are on Medicaid or have inadequate insurance. State law requires that other girls get coverage through their private insurers.

Health officials were quick to note that parental consent is required to give the vaccine.

Merck, the manufacturer of Gardasil, has backed state laws to make it easier to distribute the HPV vaccine in schools.

But it recently backed off its lobbying campaign following criticism that such laws would encourage promiscuity among youths.

Queens Councilwoman Helen Sears said an educational campaign would be needed for parents, some of whom may have moral objections to giving young girls a vaccine for HPV.